Genetic diversity and evolutionary dynamics of Senecavirus A in Brazil

Senecavirus A (SVA) is a picornavirus that was first isolated in the USA in 2002; however, there is evidence that the virus was circulating in swine herds since 1988. Despite frequent reports of vesicular disease outbreaks caused by SVA infection in swine in Brazil since 2014, there is limited data on the genetic diversity and evolution of the virus in the country. SVA was isolated from swine exhibiting vesicular lesions, with samples originating from farms or slaughterhouses across 57 municipalities in 8 Brazilian states between 2018 and 2022. We obtained 501 SVA genomes through Sanger and Oxford Nanopore sequencing. Phylogenetic analysis revealed that Brazilian SVA sequences are genetically distinct from sequences from other countries, including China, USA and Canada, and form a monophyletic cluster, indicating a common ancestor for the viruses currently circulating in Brazil. Furthermore, there are two main clusters with sequences from the Midwest and Southern regions, suggesting that SVA is evolving independently in the swine population of the country. Pairwise sequence comparisons allowed us to identify seven unique mutations with high frequency in the Brazilian SVA sequences. Notably, mutations were identified in specific regions of the capsid proteins that interact with the host cell receptor (ANTRX1) and in surface-exposed residues, suggesting potential evolutionary changes due to receptor interaction or immune pressure. Recombination analysis provided evidence of at least five recombination events among the Brazilian strains. These findings offer new insights into the evolution of SVA circulating in Brazil and into the global epidemiology/evolutionary dynamics of the virus.